HI,

When I type the following in edgeR:

> # Process raw sequences from fastq file
> x = processAmplicons("Index2.Plate_10.fastqsanger", barcodefile="Samples1.txt",
+     hairpinfile="Hairpins1-10.txt", hairpinStart=28, hairpinEnd=50, verbose=TRUE)

I get the following error:
Error in processAmplicons("Index2.Plate_10.fastqsanger", barcodefile = "Samples1.txt",  :
  Barcode sequence length is set to 5, there are barcode sequence not with specified length.

It is true my barcode length is 6 not 5. How can I change this on edgeR? I can't seem to find the script that I can edit anywhere on the edgeR program/folder.

Thanks

Try changing the barcodeEnd argument (maybe set this to 6 in your case if they are 6 bases long and start at position 1 in each read), or if need be both barcodeStart and barcodeEnd to suit the length and position of the sample indexes in your sequence reads. They need to be in a fixed position for processAmplicons to work for you though.

Thank you. I was able to change it in R. I typed:

> fix(processAmplicons)

and a window popped up where I could make edit to the script.

Thanks,

Lucia

I am so new to R that to be honest I don't know, I'll I can say is that I am not getting the problem anymore. However, this is not a permanent change because as soon as I closed the program it reverts any changes that I made to the script changes to the original format, which I can live with that.

How do you get to the function call? sorry about this silly question but I just have no background in bioinformatics.

thanks,

Lucia